Research workbench
Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with KIR6.2-ctd in the down conformation
Analyse Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TYT
- Type
- protein
- Length
- 2,759 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-sensitive inward rectifier potassium channel 11; ATP-binding cassette sub-family C…
- UniProt
- P70673, Q09427
- Ligands
- PTY, ATP, POV, P5S, BJX, NAG, K
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-sensitive inward rectifier potassium channel 11 | protein | 356 | 30% helix, 21% strand | P70673 |
| B, C, D | ATP-sensitive inward rectifier potassium channel 11 | protein | 326 | 30% helix, 25% strand | P70673 |
| E | ATP-binding cassette sub-family C member 8 | protein | 1425 | 63% helix, 6% strand | Q09427 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 6 copies · chains A, E
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, D, B, C, E
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 5 copies · chains A, D, E, B, C
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 2 copies · chains A, B, E
- BJX · Repaglinide · ligand · chains A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- K · Potassium ion · metal · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.89 | 0.91 | 114 | BJX |
| 2 | 1184 | 0.86 | 0.86 | 118 | empty |
| 3 | 1194 | 0.82 | 0.83 | 122 | empty |
| 4 | 1039 | 0.82 | 0.83 | 105 | empty |
| 5 | 1128 | 0.82 | 0.83 | 118 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2961 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 2895 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2857 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2814 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 2090 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- Q09427 · AlphaFold monomer V2.0 prediction for ATP-binding cassette sub-family C member 8 (Q09427) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P70673 · AlphaFold monomer V2.0 prediction for ATP-sensitive inward rectifier potassium channel 11… · a predicted model of the same protein · chain B against A, TM-score 0.89
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P70673
- Every structure of UniProt Q09427
- Elsewhere: RCSB PDB 7TYT · PDBe 7TYT · UniProt P70673 · UniProt Q09427
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